SNPs and Indels within Regions on Chromosome 6p and Other Parts of the Genome
| Region | HLA alleles[i] | Length kb[ii] | G + C % | Nucleotide diversity[iii] % (min, max)[iv] | Ts/Tv[v] | Indels[vi]% (<100 bp) | No. of indels (>100 bp) | Indels (>100 bp) composition |
| MHC (6p21.3) | ||||||||
| Class II[vii] | F1121[xi] vs DQB1*0201;DQA1*05011 a[xii] | 17.1 | 36.7 | 0.29 (0,3) | 22/27 (0.81) | 0.05 | 0 | |
| DQB1*0402; vs DQB1*0201;DQA1*05011 b[xii] | 24.9 | 41.6 | 5.3 (0,16) | 850/423 (2.01) | 0.30 | 5 | 3 LTR; 1 Alu; 1 L1 | |
| DQA1*05011 vs DQB1*0201;DQA1*05011 c[xii] | 37.7 | 39.3 | 0.01 (0,2) | 1/4 (0.25) | 0.005 | 0 | ||
| Class I | ||||||||
| β block | A29; B44; Cw4; DR7(44.1) vs A2;B62; Cw10; DR4(62.1) d[xii] | 138.7 | 44.8 | 0.45 (0,18) | 383/244 (1.57) | 0.07 | 4 | 2Alu; 1 SVA; 1 simple repeat |
| A29; B44; Cw4; DR7(44.1) vs A3;B8; Cw–; DR3(8.1) e[xii] | 74.2 | 45.4 | 1.3 (0,9) | 654/302 (2.17) | 0.12 | 0 | ||
| A3; B8; Cw–; DR3(8.1) vs A29; B14; Cw–; DR7(14.1) f[xii] | 160.7 | 43.1 | 0.9 (0,13) | 999/437 (2.29) | 0.04 | 4 | 2Alu; 1 SVA; 1 L1 + Alu | |
| α block | A3,29; B8, 14; Cw–,–; DR3,7(8.1;14.1) vs A2; B62; Cw10; DR4(62.1)[xiii] | 355.1 | 44.2 | 0.56 (0,10) | 1301/695 (1.87) | 0.06 | 6 | 1 L1; 1 SVA; 2 Alu; 2 simple repeat |
| SCA1 (6p23)[vii] | 467D16 vs SGII[xi] | 137.8 | 45.0 | 0.09 (0,7) | 75/48 (1.56) | 0.03 | 1 | Alu + L1 |
| TCR complex[viii] | 0.2 | |||||||
| Autosomal sequences[ix] | 0.08 | |||||||
| APOE[x] | 0.09 | |||||||
[i] Based on the assignment of ancestral haplotypes, taken from Degli-Espostl et al. (1992).
[ii] Total length of comparison minus indels.
[iii] Nucleotide diversity is given as the average number of substitutions per 100 nucleotides, corrected by Kimura's two parameter model.
[iv] Minimum and maximum nucleotide diversity from a 100-nucleotide window.
[v] Transition/transversion ratio used to calculate nucleotide diversity.
[vi] Nucleotide diversity does not include indels, which have been calculated separately. Consecutive indel sites are counted as a single event.
[vii] Taken from Horton et al. (1998).
[viii] Nucleotide diversity based on cosmid overlaps within the T cell receptor (TCR) complex, taken from Rowen et al., (1996).
[ix] Silent nucleotide diversity based on a set of autosomal sequences, taken from Li and Saddler (1991).
[x] Based on a 4-Mb SNP map around APOE, taken from Lai et al. (1998).
[xi] Clone names taken from Horton et al. (1998).
[xii] a–f correspond to Figure 1.
[xiii] The Hampe sequence does not delineate the HLA alleles of the template used for the α block sequence. Based on sequence matching of the HLA-A locus, we have designated it as the 62.1AH, taken from Degli-Esposti et al. (1992).